Journal Article

Genetic diversity, genetic structure and demographic history of Cycas simplicipinna(Cycadaceae) assessed by DNA sequences and SSR markers

Gong, Xun, Wang, Yuehua, Feng, Xiuyan

2014

Overview

Background Cycas simplicipinna (T. Smitinand) K. Hill. (Cycadaceae) is an endangered species in China. There were seven populations and 118 individuals that we could collect were genotyped in this study. Here, we assessed the genetic diversity, genetic structure and demographic history of this species. Results Analyses of data of DNA sequences (two maternally inherited intergenic spacers of chloroplast, cpDNA and one biparentally inherited internal transcribed spacer region ITS4-ITS5, nrDNA) and sixteen microsatellite loci (SSR) were conducted in the species. Of the 118 samples, 86 individuals from the seven populations were used for DNA sequencing and 115 individuals from six populations were used for the microsatellite study. We found high genetic diversity at the species level, low genetic diversity within each of the seven populations and high genetic differentiation among the populations. There was a clear genetic structure within populations of C. simplicipinna . A demographic history inferred from DNA sequencing data indicates that C. simplicipinna experienced a recent population contraction without retreating to a common refugium during the last glacial period. The results derived from SSR data also showed that C. simplicipinna underwent past effective population contraction, likely during the Pleistocene. Conclusions Some genetic features of C. simplicipinna such as having high genetic differentiation among the populations, a clear genetic structure and a recent population contraction could provide guidelines for protecting this endangered species from extinction. Furthermore, the genetic features with population dynamics of the species in our study would help provide insights and guidelines for protecting other endangered species effectively.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Agriculture / Bayes Theorem / Biomedical and Life Sciences / China / chloroplast DNA / chloroplasts / Climate change / Conservation of Natural Resources / Cycadaceae / Cycas / Cycas - genetics / data analysis / Deoxyribonucleic acid / DNA / DNA, Chloroplast - genetics / DNA, Plant - genetics / DNA, Ribosomal Spacer - genetics / Endangered species / Evolution / extinction / Extinction (Biology) / Genetic aspects / Genetic diversity / Genetic structure / Genetic Variation / Genetics and crop biotechnology / Genetics, Population / Genomics / genotyping / guidelines / Haplotypes / inheritance (genetics) / intergenic DNA / internal transcribed spacers / Life Sciences / Methods / Microsatellite Repeats / Phylogeny / Plant Sciences / Pleistocene / Population biology / population dynamics / Protected species / Protection and preservation / Research Article / Seeds / sequence analysis / Sequence Analysis, DNA / Species diversity / Species extinction / Studies / transcription (genetics) / Tree Biology / Wildlife conservation